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Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data

Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data
Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data
Quantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3-4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.
1-4
Vergara Lope Gracia, Norma Alejandra
84ea3389-86d8-4b89-ad65-729173419305
Jabalameli, M.Reza
d533e702-7a6b-4f2d-8947-352ea1dd769b
Horscroft, Clare
6ed6a58f-5fe9-4be0-a92e-bee5ea43aa8c
Ennis, Sarah
7b57f188-9d91-4beb-b217-09856146f1e9
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d
Vergara Lope Gracia, Norma Alejandra
84ea3389-86d8-4b89-ad65-729173419305
Jabalameli, M.Reza
d533e702-7a6b-4f2d-8947-352ea1dd769b
Horscroft, Clare
6ed6a58f-5fe9-4be0-a92e-bee5ea43aa8c
Ennis, Sarah
7b57f188-9d91-4beb-b217-09856146f1e9
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d

Vergara Lope Gracia, Norma Alejandra, Jabalameli, M.Reza, Horscroft, Clare, Ennis, Sarah, Collins, Andrew and Pengelly, Reuben (2019) Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data. Scientific Data, 6, 1-4, [208]. (doi:10.1038/s41597-019-0227-y).

Record type: Article

Abstract

Quantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3-4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.

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Data_Report_LD_maps - Accepted Manuscript
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s41597-019-0227-y - Version of Record
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More information

Accepted/In Press date: 29 August 2019
e-pub ahead of print date: 17 October 2019
Published date: 2019

Identifiers

Local EPrints ID: 433766
URI: http://eprints.soton.ac.uk/id/eprint/433766
PURE UUID: fb9048c9-4c8a-4502-a5f9-49ddeb9c08e6
ORCID for M.Reza Jabalameli: ORCID iD orcid.org/0000-0002-7762-0529
ORCID for Sarah Ennis: ORCID iD orcid.org/0000-0003-2648-0869
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771
ORCID for Reuben Pengelly: ORCID iD orcid.org/0000-0001-7022-645X

Catalogue record

Date deposited: 03 Sep 2019 16:30
Last modified: 09 Jan 2022 03:45

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Contributors

Author: Norma Alejandra Vergara Lope Gracia
Author: M.Reza Jabalameli ORCID iD
Author: Clare Horscroft
Author: Sarah Ennis ORCID iD
Author: Andrew Collins ORCID iD
Author: Reuben Pengelly ORCID iD

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